long-read RNA-seq quantification using isoQuant

Summary

long-read RNA-seq quantification using isoQuant 3.5.0

https://github.com/ablab/IsoQuant

Input

Fastq files. Need to have fastq in the filename. e.g., .fastq or .fastq.gz

Usage

Copy the *fastq* files into the working dir.

hpcf_interactive.sh

module load python/2.7.13

# cd to your working dir

# use gencode v47 canonical gtf, one transcript per gene, for novel transcript identification, see tequial_seq_all folder
run_lsf.py -p isoQuant

# only this run below is for nanopore, others are for Pacbio data. use gencode v47 canonical gtf
run_lsf.py -p isoQuant_nanopore

# copy all the bam files (minimap aligned) to a working dir and start from bam, this pipeline uses ISO_Tequila_JJ_all.gtf based on v47
run_lsf.py -p isoQuant_bam

Output

In the jobID folder, see OUT.transcript_grouped_tpm.tsv or OUT.gene_grouped_tpm.tsv

Comments

code @ github.